DOCSLIB.ORG

The Molecular Coupling Between Substrate Recognition and ATP Turnover in A

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Molecular Coupling Between Substrate Recognition and ATP Turnover in A bioRxiv preprint doi: https://doi.org/10.1101/2020.10.21.345918; this version posted October 21, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. The molecular coupling between substrate recognition and ATP turnover in a AAA+ hexameric helicase loader Neha Puri1,2, Amy J. Fernandez1, Valerie L. O’Shea Murray1,3, Sarah McMillan4, James L. Keck4, James M. Berger1,* 1Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205 2Bristol Myers Squibb, 38 Jackson Road, Devens, MA 01434 3Saul Ewing Arnstein & Lehr, LLP, Centre Square West, 1500 Market Street, 38th Floor, Philadelphia, PA 19102 4Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706 *Corresponding author Email: [email protected] Keywords: DNA replication, AAA+ ATPase, Helicase, Meier-Gorlin Syndrome 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.10.21.345918; this version posted October 21, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. ABSTRACT In many bacteria and in eukaryotes, replication fork establishment requires the controlled loading of hexameric, ring-shaped helicases around DNA by AAA+ ATPases. How loading factors use ATP to control helicase deposition is poorly understood. Here, we dissect how specific ATPase elements of E. coli DnaC, an archetypal loader for the bacterial DnaB helicase, play distinct roles in helicase loading and the activation of DNA unwinding. We identify a new element, the arginine-coupler, which regulates the switch- like behavior of DnaC to prevent futile ATPase cycling and maintains loader responsiveness to replication restart systems. Our data help explain how the ATPase cycle of a AAA+-family helicase loader is channeled into productive action on its target; comparative studies indicate elements analogous to the Arg-coupler are present in related, switch-like AAA+ proteins that control replicative helicase loading in eukaryotes, as well as polymerase clamp loading and certain classes of DNA transposases. INTRODUCTION The proliferation of all cells relies on the accurate and timely copying of DNA by large macromolecular assemblies termed replisomes. Cellular replisomes are complex, multi- functional assemblies that co-localize a number of essential biochemical functions to increase replication efficiency and speed (O’Donnell et al.). One such function is the unwinding of parental chromosomes to expose template DNA for leading and lagging strand synthesis, a process carried out by specialized, ring-shaped enzymes known as helicases. In Gram-negative bacteria, an enzyme known as DnaB (DnaC in Gram- positive organisms) serves as the principal helicase for driving replication fork 2 bioRxiv preprint doi: https://doi.org/10.1101/2020.10.21.345918; this version posted October 21, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. progression (reviewed in Chodavarapu and Kaguni, 2016). DnaB proteins form hexameric rings and are generally incapable of spontaneously associating with chromosomal replication start sites (origins). As a consequence, DnaB helicases are specifically recruited and deposited onto single-stranded origin DNA by dedicated initiation and loading factors. Replicative helicase loading in bacteria depends on at least one of two known types of proteins. One widespread class, comprising factors related to a protein known as DciA, is ATP-independent (Brézellec et al., 2016; Mann et al., 2017). The second class is composed of DnaC/DnaI-family proteins, which are ATP-dependent and present in model organisms such as E. coli and B. subtilis (Brézellec et al., 2016). Both DnaC and DnaI consist of an N-terminal helicase-binding domain (HBD) fused to a C-terminal AAA+ (ATPases Associated with various cellular Activities) nucleotide-binding fold (Fig. 1A) (Ludlam et al., 2001; Neuwald et al., 1999b). The AAA+ region of DnaC contains numerous signature sequence motifs (Walker A, Walker B, Sensor I & II, Arginine- finger), several of which have been reported to be critical for the function of the loader in E. coli (Makowska-Grzyska and Kaguni, 2010; Mott et al., 2008). A few of these elements have been examined and found to be important for controlling aspects of DnaC activity in vitro as well (Davey et al., 2002; Makowska-Grzyska and Kaguni, 2010; Mott et al., 2008) however, a systematic analysis of their individual mechanistic impact on the efficiency of DNA loading and unwinding by DnaB has been lacking. 3 bioRxiv preprint doi: https://doi.org/10.1101/2020.10.21.345918; this version posted October 21, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. DnaC-type loaders help place DnaB hexamers on single-stranded DNA by opening the helicase ring and allowing a nucleic acid strand to enter laterally into the pore of the complex (Arias-Palomo et al., 2019). In the context of DnaB, six DnaC protomers form a cracked hexameric oligomer, generating composite ATPase active sites at five of the six subunit interfaces (Fig. 1B,C) (Arias-Palomo et al., 2013, 2019). The AAA+ fold of DnaC binds ssDNA directly, at a site distal from its ATP-binding locus (Arias-Palomo et al., 2019; Ioannou et al., 2006; Mott et al., 2008). Prior to binding DNA, six DnaC protomers latch onto a DnaB hexamer through their HBDs to promote helicase ring opening. In this configuration, EM studies have shown that DnaB resides in an ADP-like state, and DnaC in an ATP-bound form (Arias-Palomo et al., 2019). DNA binding induces a large conformational rearrangement in the DnaB hexamer and compresses the DnaC ATPase ring, switching the ATPase status of the helicase and the loader into ATP and ADP-forms, respectively. Curiously, although DnaB helps promote the local co-association of neighboring DnaC AAA+ domains, the ATPase activity of the loader does not manifest until ssDNA is bound (Arias-Palomo et al., 2013; Davey et al., 2002; Kobori and Kornberg, 1982) How DnaB promotes DnaC self-assembly yet does not directly trigger ATPase turnover by the loader is not understood. How DNA binding is relayed to the DnaC ATPase site and whether DnaB ATPase function is important for loading (as structural work suggests) are similarly unknown. Addressing these questions is important for understanding how replicative helicase loaders exploit nucleotide-coupling mechanisms to generate productive action on client substrates, a question relevant to AAA+ ATPases in general. 4 bioRxiv preprint doi: https://doi.org/10.1101/2020.10.21.345918; this version posted October 21, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Here, we show through a structure-guided biochemical approach that defects in different DnaC ATPase elements have distinct impacts on the ability of the loader to deposit DnaB onto DNA and to activate helicase unwinding of forked substrates. DnaC is shown to be capable of promoting helicase unloading in an ATP-dependent manner; both loading and unloading are additionally found to be influenced by the ATPase activity of the helicase as well. We identify a set of residues in DnaC that couple loader ATPase activity to the binding of DnaB and ssDNA and that unexpectedly modulate the responsiveness of DnaC to a replication restart factor, and we show that analogs of one of these elements, an active-site arginine, are present in related AAA+ superfamily members that operate with switch-like properties. Our data collectively explain how the ATPase status of DnaC is coupled to recognition of its DnaB and ssDNA substrates to ensure tight coupling of helicase loading and DNA unwinding with nucleotide turnover. RESULTS: Conserved AAA+ motifs support DnaC ATPase activity We first set out to address the extent to which five canonical AAA+ motifs support the ATP-hydrolysis activity of E. coli DnaC. Using site-directed mutagenesis, we generated a panel of individual DnaC variants lacking one of the five key residues found in AAA+ proteins (Walker A – K112R; Walker B – E170Q; Sensor I – N203A; Arg-finger – R220D; Sensor II – R237D). We expressed and purified each of these mutants and, using a coupled assay, tested them for ATP hydrolysis activity in the presence of a hydrolysis defective DnaB mutant (DnaBKAEA) and ssDNA. The ablation of any of the five residues was found to result in complete loss of ATPase function (Fig 2A). These results highlight 5 bioRxiv preprint doi: https://doi.org/10.1101/2020.10.21.345918; this version posted October 21, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. the importance of the AAA+ signature residues to the nucleotide turnover capabilities of E. coli DnaC, and further establish that the hydrolysis activity present in the assay derives from the loader and not the helicase or a contaminating ATPase.
Load more

Recommended publications
  • Specific Binding of Transposase to Terminal Inverted Repeats Of
    Proc. Natl. Acad. Sci. USA Vol. 84, pp. 8220-8224, December 1987 Biochemistry Specific binding of transposase to terminal inverted repeats of transposable element Tn3 (transposon/DNA binding protein/DNase I "footprinting") HITOSHI ICHIKAWA*, KAORU IKEDA*, WILLIAM L. WISHARTt, AND EIICHI OHTSUBO*t *Institute of Applied Microbiology, University of Tokyo, Bunkyo-ku, Yayoi 1-1-1, Tokyo 113, Japan; and tDepartment of Molecular Biology, Princeton University, Princeton, NJ 08544 Communicated by Norman Davidson, July 27, 1987 ABSTRACT Tn3 transposase, which is required for trans- containing the Tn3 terminal regions when 8 mM ATP is position of Tn3, has been purified by a low-ionic-strength- present (14). precipitation method. Using a nitrocellulose filter binding In this paper, we study the interaction of Tn3 transposase, assay, we have shown that transposase binds to any restriction which has been purified by a low-ionic-strength-precipitation fragment. However, binding of the transposase to specific method, with DNA. We demonstrate that the purified fragments containing the terminal inverted repeat sequences of transposase is an ATP-independent DNA binding protein, Tn3 can be demonstrated by treatment of transposase-DNA which has interesting properties that may be involved in the complexes with heparin, which effectively removes the actual transposition event of Tn3. transposase bound to the other nonspecific fragments at pH 5-6. DNase I "footprinting" analysis showed that the MATERIALS AND METHODS transposase protects an inner 25-base-pair region of the 38- base-pair terminal inverted repeat sequence of Tn3. This Bacterial Strains and Plasmids. The bacterial strains used protection is not dependent on pH.
    [Show full text]
  • Replisome Assembly at Oric, the Replication Origin of E. Coli, Reveals an Explanation for Initiation Sites Outside an Origin
    Molecular Cell, Vol. 4, 541±553, October, 1999, Copyright 1999 by Cell Press Replisome Assembly at oriC, the Replication Origin of E. coli, Reveals an Explanation for Initiation Sites outside an Origin Linhua Fang,*§ Megan J. Davey,² and Mike O'Donnell²³ have not been addressed. For example, is the local un- *Microbiology Department winding sufficiently large for two helicases to assemble Joan and Sanford I. Weill Graduate School of Medical for bidirectional replication, or does one helicase need Sciences of Cornell University to enter first and expand the bubble via helicase action New York, New York 10021 to make room for the second helicase? The known rep- ² The Rockefeller University and licative helicases are hexameric and encircle ssDNA. Howard Hughes Medical Institute Which strand does the initial helicase(s) at the origin New York, New York 10021 encircle, and if there are two, how are they positioned relative to one another? Primases generally require at least transient interaction with helicase to function. Can Summary primase function with the helicase(s) directly after heli- case assembly at the origin, or must helicase-catalyzed This study outlines the events downstream of origin DNA unwinding occur prior to RNA primer synthesis? unwinding by DnaA, leading to assembly of two repli- Chromosomal replicases are comprised of a ring-shaped cation forks at the E. coli origin, oriC. We show that protein clamp that encircles DNA, a clamp-loading com- two hexamers of DnaB assemble onto the opposing plex that uses ATP to assemble the clamp around DNA, strands of the resulting bubble, expanding it further, and a DNA polymerase that binds the circular clamp, yet helicase action is not required.
    [Show full text]
  • Initiation of Enzymatic Replication at the Origin of the Escherichia
    Proc. Nati. Acad. Sci. USA Vol. 82, pp. 3954-3958, June 1985 Biochemistry Initiation of enzymatic replication at the origin of the Escherichia coli chromosome: Primase as the sole priming enzyme (DNA/orC/plasmids) ARIE VAN DER ENDEt, TANIA A. BAKER, TOHRU OGAWA*, AND ARTHUR KORNBERG Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305 Contributed by Arthur Kornberg, January 28, 1985 ABSTRACT The enzymatic replication of plasmids con- MATERIALS AND METHODS taining the unique (245 base pair) origin of the Escherichia coli chromosome (oriC) can be initiated with any of three enzyme DNAs and Reagents. pCM959 (4) was a gift from M. Meijer priming systems: primase alone, RNA polymerase alone, or (University of Amsterdam, The Netherlands); pTOA7 (T. both combined (Ogawa, T., Baker, T. A., van der Ende, A. & Ogawa) was constructed by inserting the Hae II-Acc I Kornberg, A. (1985) Proc. Natl. Acad. Sci. USA 82, oriC-containing fragment from M13oriC26 (7) via EcoRI 3562-3566). At certain levels of auxiliary proteins linkers into EcoRI-cleaved pMAPCdSG10, a deletion deriva- (topoisomerase I, protein HU, and RNase H), the solo primase tive of pBR327 (W. A. Segraves, personal communication); system is efficient and responsible for priming synthesis of all pSY317, M13oriC26, M13oriC2LB5, and M13AE101 are DNA strands. Replication of oriC plasmids is here separated described in Table 1 and elsewhere (3, 7). Tricine, creatine into four stages: (i) formation of an isolable, prepriming phosphate, ribo- and deoxyribonucleoside triphosphates complex requiring oriC, dnaA protein, dnaB protein, dnaC (rNTPs and dNTPs) were from Sigma; a-32P-labeled dTTP, protein, gyrase, single-strand binding protein, and ATP; (ii) rATP, rUTP, rGTP, and rCTP (>400 Ci/mmol; 1 Ci = 37 formation of a primed template by primase; (iii) rapid, GBq) were from Amersham.
    [Show full text]
  • A Sleeping Beauty Mutagenesis Screen Reveals a Tumor Suppressor Role for Ncoa2/Src-2 in Liver Cancer
    A Sleeping Beauty mutagenesis screen reveals a tumor suppressor role for Ncoa2/Src-2 in liver cancer Kathryn A. O’Donnella,b,1,2, Vincent W. Kengc,d,e, Brian Yorkf, Erin L. Reinekef, Daekwan Seog, Danhua Fanc,h, Kevin A. T. Silversteinc,h, Christina T. Schruma,b, Wei Rose Xiea,b,3, Loris Mularonii,j, Sarah J. Wheelani,j, Michael S. Torbensonk, Bert W. O’Malleyf, David A. Largaespadac,d,e, and Jef D. Boekea,b,i,2 Departments of aMolecular Biology and Genetics, iOncology, jDivision of Biostatistics and Bioinformatics, and kPathology, and bThe High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21205; cMasonic Cancer Center, dDepartment of Genetics, Cell Biology, and Development, eCenter for Genome Engineering, and hBiostatistics and Bioinformatics Core, University of Minnesota, Minneapolis, MN 55455; fDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030; and gLaboratory of Experimental Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 AUTHOR SUMMARY Emerging data from cancer ge- functions are altered. This ap- fi nome-sequencing studies have Sleeping Beauty (SB) transposase proach identi ed at least 16 demonstrated that human genes/loci that contribute to liver tumors exhibit tremendous Transposon array with gene trap (GT) tumor development. complexity and heterogeneity in We next validated that the the number and nature of iden- genes identified in the SB screen tified mutations (1). Based on contribute to tumor initiation these findings, there is an in- SB mobilization and/or progression using in vitro creasing need for in vivo vali- and in vivo cancer model sys- dation of genes whose altered tems.
    [Show full text]
  • RNA As a Source of Transposase for Sleeping Beauty-Mediated Gene Insertion and Expression in Somatic Cells and Tissues
    doi:10.1016/j.ymthe.2005.10.014 SHORT COMMUNICATION RNA as a Source of Transposase for Sleeping Beauty-Mediated Gene Insertion and Expression in Somatic Cells and Tissues Andrew Wilber,1 Joel L. Frandsen,1 Jennifer L. Geurts,1 David A. Largaespada,1 Perry B. Hackett,1,2 and R. Scott McIvor1,* 1The Arnold and Mabel Beckman Center for Transposon Research, Gene Therapy Program, Institute of Human Genetics, and Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA 2Discovery Genomics, Inc., Minneapolis, MN 55455, USA *To whom correspondence and reprint requests should be addressed at The Department of Genetics, Cell Biology, and Development, 6-160 Jackson Hall, 321 Church Street SE, University of Minnesota, Minneapolis, MN 55455, USA. Fax: +1 612 625 9810. E-mail: [email protected]. Available online 20 December 2005 Sleeping Beauty (SB) is a DNA transposon capable of mediating gene insertion and long-term expression in vertebrate cells when co-delivered with a source of transposase. In all previous reports of SB-mediated gene insertion in somatic cells, the transposase component has been provided by expression of a co-delivered DNA molecule that has the potential for integration into the host cell genome. Integration and continued expression of a gene encoding SB transposase could be problematic if it led to transposon re-mobilization and re-integration. We addressed this potential problem by supplying the transposase-encoding molecule in the form of mRNA. We show that transposase-encoding mRNA can effectively mediate transposition in vitro in HT1080 cells and in vivo in mouse liver following co-delivery with a recoverable transposon or with a luciferase transposon.
    [Show full text]
  • Licensing RNA-Guided Genome Defense
    TIBS-1023; No. of Pages 10 Review Recognizing the enemy within: licensing RNA-guided genome defense Phillip A. Dumesic and Hiten D. Madhani Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA How do cells distinguish normal genes from transpo- RNAi-related RNA silencing pathways are deeply con- sons? Although much has been learned about RNAi- served genome defense mechanisms that act in organisms related RNA silencing pathways responsible for genome from protist to human to recognize and suppress transpo- defense, this fundamental question remains. The litera- sons [8]. In all of these pathways, 20–30 nucleotide small ture points to several classes of mechanisms. In some RNAs act in complex with Argonaute family proteins to cases, double-stranded RNA (dsRNA) structures pro- silence complementary transcripts. Depending on the duced by transposon inverted repeats or antisense inte- pathway and context, silencing proceeds by a variety of gration trigger endogenous small interfering RNA mechanisms, which include RNA degradation, translation- (siRNA) biogenesis. In other instances, DNA features al repression, and the establishment of repressive histone associated with transposons – such as their unusual modifications [9,10]. The pathways also differ in the means copy number, chromosomal arrangement, and/or chro- by which they generate small RNAs. In the canonical RNAi matin environment – license RNA silencing. Finally, re- pathway, RNase-III-type Dicer enzymes convert long cent studies have identified improper transcript dsRNA into small interfering RNA (siRNA). In contrast, processing events, such as stalled pre-mRNA splicing, PIWI-interacting RNA (piRNA) pathways do not require as signals for siRNA production.
    [Show full text]
  • Crystal Structure of the Bloom's Syndrome Helicase Indicates a Role
    Nucleic Acids Research Advance Access published April 21, 2015 Nucleic Acids Research, 2015 1 doi: 10.1093/nar/gkv373 Crystal structure of the Bloom’s syndrome helicase indicates a role for the HRDC domain in conformational changes Joseph A. Newman1,†, Pavel Savitsky1,†, Charles K. Allerston1, Anna H. Bizard2, Ozg¨ un¨ Ozer¨ 2, Kata Sarlos´ 2, Ying Liu2, Els Pardon3,4, Jan Steyaert3,4, Ian D. Hickson2 and Opher Gileadi1,* 1Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK, 2Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Building 18.1, Blegdamsvej 3B, 2200 Copenhagen N, Denmark, 3Structural Biology Downloaded from Brussels, Vrije Universiteit Brussel, Pleinlaan 2 , 1050 Brussels, Belgium and 4Structural Biology Research Center, VIB, Brussel, Pleinlaan 2, 1050 Brussels, Belgium Received January 13, 2015; Revised March 27, 2015; Accepted April 03, 2015 http://nar.oxfordjournals.org/ ABSTRACT some instability, including chromatid gaps and breaks (4), various chromosome structural rearrangements (5)andan Bloom’s syndrome helicase (BLM) is a member of the increase in the number of sister chromatid exchange (SCE) RecQ family of DNA helicases, which play key roles in events, the latter serving as a distinguishing feature for the the maintenance of genome integrity in all organism clinical diagnosis of BS (6). groups. We describe crystal structures of the BLM Bloom’s syndrome helicase (BLM), like all RecQ-family helicase domain in complex with DNA and with an an- helicases, acts as a 3 to 5 helicase (7) on a wide variety tibody fragment, as well as SAXS and domain asso- of DNA substrates including forked duplexes, G quadru- at Chadwick & RAL Libraries on April 23, 2015 ciation studies in solution.
    [Show full text]
  • Neurofibromin Controls Macropinocytosis and Phagocytosis
    RESEARCH ARTICLE elifesciences.org Neurofibromin controls macropinocytosis and phagocytosis in Dictyostelium Gareth Bloomfield1*, David Traynor1, Sophia P Sander1,2, Douwe M Veltman1, Justin A Pachebat3,4, Robert R Kay1 1MRC Laboratory of Molecular Biology, Cambridge, United Kingdom; 2Centre for Human Development, Stem Cells and Regeneration, University of Southampton, Southampton, United Kingdom; 3Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom; 4Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom Abstract Cells use phagocytosis and macropinocytosis to internalise bulk material, which in phagotrophic organisms supplies the nutrients necessary for growth. Wildtype Dictyostelium amoebae feed on bacteria, but for decades laboratory work has relied on axenic mutants that can also grow on liquid media. We used forward genetics to identify the causative gene underlying this phenotype. This gene encodes the RasGAP Neurofibromin (NF1). Loss of NF1 enables axenic growth by increasing fluid uptake. Mutants form outsized macropinosomes which are promoted by greater Ras and PI3K activity at sites of endocytosis. Relatedly, NF1 mutants can ingest larger-than-normal particles using phagocytosis. An NF1 reporter is recruited to nascent macropinosomes, suggesting that NF1 limits their size by locally inhibiting Ras signalling. Our results link NF1 with macropinocytosis and phagocytosis for the first time, and we propose that NF1 evolved in early phagotrophs to spatially modulate Ras activity, thereby constraining and shaping their feeding structures. DOI: 10.7554/eLife.04940.001 *For correspondence: garethb@ mrc-lmb.cam.ac.uk Introduction Phagotrophic cells feed by performing large-scale endocytosis. A wide range of unicellular Competing interests: The eukaryotes grow in this way, suggesting that it is extremely old in evolutionary terms (Stanier, authors declare that no 1970; Cavalier-Smith, 2002; Yutin et al., 2009).
    [Show full text]
  • SUPPLEMENTARY INFORMATION in Silico Signature Prediction
    SUPPLEMENTARY INFORMATION In Silico Signature Prediction Modeling in Cytolethal Distending Toxin-Producing Escherichia coli Strains Maryam Javadi, Mana Oloomi*, Saeid Bouzari Department of Molecular Biology, Pasteur Institute of Iran, Tehran 13164, Iran http://www.genominfo.org/src/sm/gni-15-69-s001.pdf Supplementary Table 6. Aalphabetic abbreviation and description of putative conserved domains Alphabetic Abbreviation Description 17 Large terminase protein 2_A_01_02 Multidrug resistance protein 2A0115 Benzoate transport; [Transport and binding proteins, Carbohydrates, organic alcohols] 52 DNA topisomerase II medium subunit; Provisional AAA_13 AAA domain; This family of domains contain a P-loop motif AAA_15 AAA ATPase domain; This family of domains contain a P-loop motif AAA_21 AAA domain AAA_23 AAA domain ABC_RecF ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase ABC_SMC_barmotin ATP-binding cassette domain of barmotin, a member of the SMC protein family AcCoA-C-Actrans Acetyl-CoA acetyltransferases AHBA_syn 3-Amino-5-hydroxybenzoic acid synthase family (AHBA_syn) AidA Type V secretory pathway, adhesin AidA [Cell envelope biogenesis] Ail_Lom Enterobacterial Ail/Lom protein; This family consists of several bacterial and phage Ail_Lom proteins AIP3 Actin interacting protein 3; Aip3p/Bud6p is a regulator of cell and cytoskeletal polarity Aldose_epim_Ec_YphB Aldose 1-epimerase, similar to Escherichia coli YphB AlpA Predicted transcriptional regulator [Transcription] AntA AntA/AntB antirepressor AraC AraC-type
    [Show full text]
  • Molecular Switch-Like Regulation Enables Global Subunit Coordination in a Viral Ring Atpase
    Molecular switch-like regulation enables global subunit coordination in a viral ring ATPase Sara Tafoyaa,b,c, Shixin Liud, Juan P. Castilloa,b, Rockney Atze,f, Marc C. Moraisg, Shelley Grimese,f,1, Paul J. Jardinee,f, and Carlos Bustamantea,b,c,h,i,j,k,l,2 aJason L. Choy Laboratory of Single Molecule Biophysics, University of California, Berkeley, CA 94720; bHoward Hughes Medical Institute, University of California, Berkeley, CA 94720; cBiophysics Graduate Group, University of California, Berkeley, CA 94720; dLaboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY 10065; eInstitute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455; fDepartment of Diagnostic and Biological Sciences, University of Minnesota, Minneapolis, MN 55455; gSealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555; hDepartment of Molecular and Cell Biology, University of California, Berkeley, CA 94720; iDepartment of Physics, University of California, Berkeley, CA 94720; jDepartment of Chemistry, University of California, Berkeley, CA 94720; kCalifornia Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720; and lKavli Energy Nanoscience Institute, University of California, Berkeley, CA 94720 Edited by Ken A. Dill, Stony Brook University, Stony Brook, NY, and approved June 15, 2018 (received for review February 20, 2018) Subunits in multimeric ring-shaped motors must coordinate their the φ29 ring ATPase can be thought of as five molecular switches activities to ensure correct and efficient performance of their arranged in a closed configuration. Moreover, the enzymatic activity mechanical tasks. Here, we study WT and arginine finger mutants of one of the subunits is up-regulated compared with the other four, of the pentameric bacteriophage φ29 DNA packaging motor.
    [Show full text]
  • Glycolytic Pyruvate Kinase Moonlighting Activities in DNA Replication
    Glycolytic pyruvate kinase moonlighting activities in DNA replication initiation and elongation Steff Horemans, Matthaios Pitoulias, Alexandria Holland, Panos Soultanas, Laurent Janniere To cite this version: Steff Horemans, Matthaios Pitoulias, Alexandria Holland, Panos Soultanas, Laurent Janniere. Gly- colytic pyruvate kinase moonlighting activities in DNA replication initiation and elongation. 2020. hal-02992157 HAL Id: hal-02992157 https://hal.archives-ouvertes.fr/hal-02992157 Preprint submitted on 10 Dec 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Glycolytic pyruvate kinase moonlighting activities in DNA replication initiation and elongation Steff Horemans1, Matthaios Pitoulias2, Alexandria Holland2, Panos Soultanas2¶ and Laurent Janniere1¶ 1 : Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France 2 : Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK Short title: PykA moonlighting activity in DNA replication Key Words: DNA replication; replication control; central carbon metabolism; glycolytic enzymes; replication enzymes; cell cycle; allosteric regulation. ¶ : Corresponding authors Laurent Janniere: [email protected] Panos Soultanas : [email protected] 1 SUMMARY Cells have evolved a metabolic control of DNA replication to respond to a wide range of nutritional conditions.
    [Show full text]
  • The GAP Arginine Finger Movement Into the Catalytic Site of Ras Increases the Activation Entropy
    The GAP arginine finger movement into the catalytic site of Ras increases the activation entropy Carsten Ko¨ tting†, Angela Kallenbach†, Yan Suveyzdis†, Alfred Wittinghofer‡, and Klaus Gerwert†§ †Lehrstuhl fu¨r Biophysik, Ruhr-Universita¨t Bochum, D-44780 Bochum, Germany; and ‡Max-Planck-Institut fu¨r Molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany Edited by Robert H. Austin, Princeton University, Princeton, NJ, and approved February 14, 2008 (received for review December 28, 2007) Members of the Ras superfamily of small G proteins play key roles the GAP-mediated catalysis as a prerequisite for a rational drug in signal transduction pathways, which they control by GTP hy- development (8). drolysis. They are regulated by GTPase activating proteins (GAPs). The key residue for GAP-mediated catalysis is the so-called Mutations that prevent hydrolysis cause severe diseases including ‘‘arginine finger’’ (9). In the x-ray structure of the Ras⅐GDP⅐ cancer. A highly conserved ‘‘arginine finger’’ of GAP is a key AlF3⅐RasGAP complex mimicking the transition state, it points residue. Here, we monitor the GTPase reaction of the Ras⅐RasGAP into the GTP binding site of Ras. It stabilizes the position of the complex at high temporal and spatial resolution by time-resolved catalytic Gln-61 and neutralizes negative charge on the phos- FTIR spectroscopy at 260 K. After triggering the reaction, we phates (10). The catalytic arginine finger is a highly conserved observe as the first step a movement of the switch-I region of Ras motive among several GAP proteins for small G proteins (11). from the nonsignaling ‘‘off’’ to the signaling ‘‘on’’ state with a rate The participation of an arginine in phosphoryl transfer as seen of3s؊1.
    [Show full text]